At first glance, I'm really liking KeepNote. It looks ideal for what I want it to do, which is to organize my thoughts and provide a ways for me to keep track of the organization. My only hesitancy at this point is that it hasn't been updated since 2012. It seems abandoned. Is that not an issue?
Long-term? It could be an issue. But it's open source project, even if author will not ever return to it, it's quite likely that some other programmer(s) will expand upon it. Perhaps some already did, since KeepNote works for me I didn't really look much further. You might like Tomboy instead if you want it more current, here is a description Other thing I have used was using was Emacs with org-mode. While current and actively developed (both org-mode extension and Emacs text editor) I can't really recommend it to you, since it's one of those "takes time to master, but it's worth in the end" types of deal.